Assassin's Creed: messages and tips

I am a fan of the Assassin's Creed series and whenever I find something interesting or useful I'll add it here.

The early Assassin's Creed games contained hidden messages from Subject 16. Most of them point towards historical events and could easily be used to form conspiracy theories.
The first messages can be found at the end of AC1 and the beginning of AC2. The remaining messages are located inside glyphs (AC2) and rifts (AC3) in the form of binary code, morse code, pigpen ciphers and Caesar shifts.

I have added my personal notes based on internet research of what the messages could mean. Each code also come with a solution.